SMTL ID : 4peg.1 (4 other biounits)

Dbr1 in complex with guanosine-5'-monophosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 5 residues within 4Å: Chain A: D.45, N.90, H.180, H.230 Ligands: 5GP.2 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: A:D.45, A:H.180, A:H.230, 5GP.2, H2O.5

1 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

5GP.2: 11 residues within 4Å: Chain A: D.45, N.90, H.91, G.201, F.202, D.205, L.209, H.230, M.231, H.232 Ligands: MN.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.201, A:H.232 Water bridges: A:G.210, A:G.210 Salt bridges: A:H.91, A:D.205, A:H.230, A:H.232

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 5 residues within 4Å: Chain A: R.50, Y.57, N.95, H.99, P.146 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.95 Water bridges: A:R.50, A:R.50, A:R.50 Salt bridges: A:R.50, A:H.99

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: S.38, L.83, N.122, K.266, T.267 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.38, A:N.122, A:T.267, A:T.267 Water bridges: A:D.268

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Montemayor, E.J. et al., Structural basis of lariat RNA recognition by the intron debranching enzyme Dbr1. Nucleic Acids Res. (2014)

Release Date

2014-08-27

Peptides

RNA lariat debranching enzyme, putative: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RNA lariat debranching enzyme, putative

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